Comparison of fatty acid content and DNA homology of the filamentous gliding bacteriaVitreoscilla,Flexibacter, Filibacter

DNA hybridization experiments showed that there was a high degree of homology amongVitreoscilla strains but not with DNA fromFilibacter limicola. Flexibacter spp were much more heterogeneous indicating a low genetic similarity. These results were also reflected in the membrane fatty acids of the bacteria. TheVitreoscilla strains were very similar with the 16:17c fatty acid being dominant. The membrane fatty acids ofF. limicola were dominated by a15:0 and a17:0 components which provided additional support for its relatedness to the genusBacillus. There was much greater diversity in the fatty acid patterns of theFlexibacter spp.F. aurantiacus, F. ruber andF. elegans shared the common dominant fatty acids 16:17c with theVitreoscilla strains, but this was replaced by the 16:16c acid inF. flexilis. F. ruber was distinguished by the absence of branched odd-chain monounsaturated fatty acids andF. elegans by the dominance of the -OH i15:0 acid. Precise determination of fatty acid double bond positions and geometry are essential for correct interpretation of increasingly complex ecological and taxonomic data sets.     

The Vitreoscilla hemoglobin gene: Molecular cloning, nucleotide sequence and genetic expression in Escherichia coli

Summary Vitreoscilla hemoglobin is involved in oxygen metabolism of this bacterium, possibly in an unusual role for a microbe. We have isolated the Vitreoscilla hemoglobin structural gene from a pUC19 genomic library using mixed oligodeoxy-nucleotide probes based on the reported amino acid sequence of the protein. The gene is expressed in Escherichia coli from its natural promoter as a major cellular protein. The nucleotide sequence, which is in complete agrecment with the known amino acid sequence of the protein, suggests the existence of promoter and ribosome binding sites with a high degree of homology to consensus E. coli upstream sequences. In the case of at least some amino acids, a codon usage bias can be detected which is different from the biased codon usage pattern in E. coli. The down-stream sequence exhibits homology with the 3 end sequences of several plant leghemoglobin genes. E. coli cells expressing the gene contain greater than fivefold more heme than controls.     

A heterotrophic bacterium inhibits growth of several species of the genus Chlorobium

A gram-negative bacterium (designed as strain BF 9500) causing growth inhibition zones on cell lawns of the anoxygenic phototrophic bacterium Chlorobium limicola BF 8000 was isolated from Lake Cisó (Spain). Strain BF 9500, identified as Stenotrophomonas maltophilia, caused growth inhibition zones on cell lawns of several strains of C. limicola except C. limicola DSM 245. It also inhibited other Chlorobium species and several heterotrophic bacteria. However, it had no effect on the growth of the eleven strains of Chromatiaceae tested. Strain BF 9500 caused the lysis of C. limicola BF 8000, whose cells formed “ghosts”. To date, this is the first report of a bacterium causing the lysis of species of the genus Chlorobium. Received: 15 August 1996 / Accepted: 15 January 1997     

Effects of nutrient addition on phytoplankton in Lake Nakanuma,Japan I. Changes in biochemical components

Effects of nutrient conditions on biochemical components (sugars and amino acids) of phytoplankton were examined in Lake Nakanuma in Japan. Phosphate, ammonium and silicate were added to water samples collected at 0 m, which were incubated for 15 days in situ. Chlorophyll a in phosphate-added samples increased much more than that in other samples. Total amino acids and total neutral sugars in phosphate-added samples also increased more than those in other samples. The increase of total amino acids and chlorophyll began faster than that of total neutral sugars during the first 5 days of incubation. Total neutral sugars in the phosphate-added samples increased rapidly after 8 days. The composition of amino acids did not change so much. However, the composition of neutral sugars changed according to the different nutrient addition. Phosphate-added samples changed greatly during the incubation. These changes were explained at least partly by changes in nutrient conditions. Addition of limiting nutrients decreased glucose content, whereas depletion of nutrients increased the content. This study indicates that measurements of the biochemical components contribute to the analysis of effects of nutrients on phytoplankton in natural waters.     

Microbiological studies of Tokyo Bay

The generic composition of the heterotrophic bacterial population of Tokyo Bay, which is now highly polluted and eutrophic, was compared with that of the adjacent, less polluted regions of Sagami Bay and Suruga Bay. Members of Vibrionaceae predominated in the bacterial flora of seawater and zooplankton samples from Sagami Bay, Suruga Bay, and the mouth of Tokyo Bay. However,Vibrio spp. formed only a small proportion of the bacterial population of the water and sediment samples from the inner Tokyo Bay; there the Gram-negative, nonmotile, nonpigmented bacteria, which were tentatively identified asAcinetobacter, were predominant. The result of experiments, in which seawater samples from Tokyo Bay were incubated under various experimental conditions, indicated that two significant factors apparently control the growth ofVibrio spp. in seawater; (1) a direct antagonism betweenVibrios and phytoplankton undergoing rapid growth, and (2) a limiting organic nutrient forvibrios.     

Effect of Growth Conditions on Yield and Heme Content of Vitreoscilla

Vitreoscilla, a gliding bacterium in the Beggiatoaceae, is an obligate aerobe in which cytochrome o functions as the terminal oxidase. Protoheme IX is the only heme type present in this organism. The yield and heme content of Vitreoscilla cells grown in yeast extract, peptone, and acetate were dependent on growth conditions. Cells harvested in early stationary phase contained roughly three times as much heme as cells in early log phase. There was an optimal shaking rate for maximum heme content of cells harvested in stationary phase at fixed initial nutrient concentration. The heme content of cells grown at a fixed shaking rate increased from 5 nmol/g (wet weight) in media which had low nutrient concentration to a maximum of 45 nmol/g (wet weight) in media which had high nutrient concentration, and there was a corresponding sixfold increase in cytochrome o content and an eightfold increase in respiratory rate, evidence that some of the additional heme was incorporated into respiratory pigments. Heme content may be controlled jointly by competition for oxygen and availability of nutrients. Temperature and initial pH affected the growth rate but not the final yield or heme content. Growth rate was optimal at pH 8.0 to 8.5. A defined medium for Vitreoscilla, which is based on glutamate as the carbon source, is described; the other organic components of this medium are acetate, tryptophan, thiamine, biotin, and riboflavin.     

Some aspects of relation between nitrogen metabolism inPisum sativum and mineral nutrition

Summary Plants ofPisum sativum grown in water culture were subjected to deficiencies in the macronutrients N, P, K, S, Ca, Mg, substitution of ammonium for nitrate and change in pH to pH 3 or 9. Free amino acids, soluble nitrogen, protein and glutamate dehydrogenase activity of shoots were measured for all nutrient types. Changes in amino acid concentrations correlated well with changes in glutamate dehydrogenase. It is considered whether this enzyme is indicative of the nutritional state of plants.     

Physiology, phylogenetic relationships, and ecology of filamentous sulfate-reducing bacteria (genus Desulfonema)

Microscopy of organic-rich, sulfidic sediment samples of marine and freshwater origin revealed filamentous, multicellular microorganisms with gliding motility. Many of these neither contained sulfur droplets such as the Beggiatoa species nor exhibited the autofluorescence of the chlorophyll-containing cyanobacteria. A frequently observed morphological type of filamentous microorganism was enriched under anoxic conditions in the dark with isobutyrate plus sulfate. Two strains of filamentous, gliding sulfate-reducing bacteria, Tokyo 01 and Jade 02, were isolated in pure cultures. Both isolates oxidized acetate and other aliphatic acids. Enzyme assays indicated that the terminal oxidation occurs via the anaerobic C₁ pathway (carbon monoxide dehydrogenase pathway). The 16S rRNA genes of the new isolates and of the two formerly described filamentous species of sulfate-reducing bacteria, Desulfonema limicola and Desulfonema magnum, were analyzed. All four strains were closely related to each other and affiliated with the δ-subclass of Proteobacteria. Another close relative was the unicellular Desulfococcus multivorans. Based on phylogenetic relationships and physiological properties, Strains Tokyo 01 and Jade 02 are assigned to a new species, Desulfonema ishimotoi. A new, fluorescently labeled oligonucleotide probe targeted against 16S rRNA was designed so that that it hybridized specifically with whole cells of Desulfonema species. Filamentous bacteria that hybridized with the same probe were detected in sediment samples and in association with the filamentous sulfur-oxidizing bacterium Thioploca in its natural habitat. We conclude that Desulfonema species constitute an ecologically significant fraction of the sulfate-reducing bacteria in organic-rich sediments and microbial mats. Received: 30 December 1998 / Accepted: 19 July 1999     

Foraminifera may structure meiobenthic communities

The cosmopolitan benthic foraminiferan, Ammonia beccarii, is a fervent microfloral predator which often forms densely-populated 2–4 cm² aggregates in the field. Sediments within aggregate patches become extensively pelletized, mucus bound and depleted in microfloral food. On a West German Wattenmeer mudflat, copepodite and naupliar densities of a predominant harpacticoid copepod, Amphiascoides limicola, were significantly depressed in sediments containing>100 A. beccarii·3 cm^-2 suggesting a possible foraminiferal: copepod amensalism. Therefore, I cultured A. beccarii and A. limicola separately in sediment microcosms and then tested if A. limicola's seemingly negative reaction to sediments containing A. beccarii occurs under controlled conditions, how various life stages of A. limicola are affected, and what the repulsive mechanisms of A. beccarii may be. In natural field sediments seeded with a latin-square dispersion of sterile sediment patches containing 0 or 100 A. beccarii, mean A. limicola naupliar and copepodite densities were 2 to 6 times lower in Ammonia-rich patches than Ammonia-poor patches (i.e. patches containing <100 A. beccarii·3 cm^-2). Choice experiments directly testing potential A. beccarii inhibitory mechanisms were conducted with A. limicola copepodites: Cubic microcosms containing a latin-square patch dispersion of (1) sterile sediments (SS) seeded with 100 A. beccarii (low microflora), (2) SS bound with sterile mucus (0.0001%) (low microflora), (3) SS seeded with pelletized sediments (high microflora), and (4) SS seeded with mucus and pellets (high microflora), showed that copepodites colonized 12 & 3, but 1 & 4 were not significantly different. Mucus addition by itself, in the absence of pelletization and microflora, strongly facilitated colonization—as did addition of microfloral-rich pelletized sediments. Pelletization and mucousbinding combined, but with low microflora, were least attractive to A. limicola. Pelletization and mucous-binding combined, but with high microflora, were more attractive to A. limicola than its complement, but not significantly so. Thus A. beccarii's inhibition of A. limicola is probably not caused by sediment pelletization and simple mucous exudates but by local microfloral depletion within aggregate foraminiferal patches.Contribution No 774 of the Belle W. Baruch Institute for Marine Biology and Coastal Research     

Production of <Emphasis Type="SmallCaps">l</Emphasis>-asparaginase in<Emphasis Type="Italic"> Enterobacter aerogenes</Emphasis> expressing<Emphasis Type="Italic"> Vitreoscilla</Emphasis> hemoglobin for efficient oxygen uptake

This study is the first utilizing Vitreoscilla hemoglobin in a heterologous bacterium, Enterobacter aerogenes, to determine the effect of such a highly efficient oxygen-uptake system on the production of l-asparaginase, an enzyme that has attracted considerable attention due to its anti-tumor activity. Here, we show that the Vitreoscilla hemoglobin expressing strain has from 10-fold to more than two orders of magnitude lower l-asparaginase activity than the wild type or the control without the Vitreoscilla hemoglobin gene under different aeration conditions. Aeration and agitation were also determining factors for enzyme production. The enzyme activity was reduced considerably under both full aerobic and anaerobic conditions, while the highest enzyme activity was determined in cultures under low aeration and low agitation. Also, the effect of different concentrations of glucose on enzyme production showed catabolic repression. Glucose at 1% caused almost total inhibition of enzyme activity, while at 0.1% it showed a slightly stimulatory effect on enzyme production, compared with glucose-free medium.     

Performance of Sparganium emersum Rehm. shoots in response to sediment quality

Biomass, dry matter production, nutrient (N, P, K, Ca, Mg) contents and accumulation were studied in Sparganium emersum Rehm. in Southern Bohemia, Czech Republic. The aim was to determine the species' relationship to sediment quality and water flow and to estimate its nutrient uptake from sediments. The plants were sampled from six field sites, and one cultivation experiment was carried out. In the field, dry weight, shoot length and leaf number related to one another, while probably responding to nutrient supply both from water and sediment, while leaf width seemed to be correlated with other environmental factors. In the experiment, all measured growth parameters, except for the number of leaves, reflected sediment quality. The standing stocks of N, P and K reflected best the sediment nutrient contents in the field, both in running and standing water, but the stocks were generally higher in running water. In the experiment, all the measured growth parameters were correlated with sediment nutrient contents, and for N and P they were also with these nutrient contents in the plants. Nutrient removal from the rooting media was substantial for nitrogen. S. emersum was found to grow well in sediments rich both in mineral nutrients and organic matter.     

Sediment and phytoplankton records of the cyanobacterial genus Anabaena in boreal Lake Pyhäjärvi

Past occurrence and quantities of Anabaena cyanobacteria in Lake Pyhäjärvi, SW Finland, were investigated using sediment and phytoplankton records. A short sediment core covering the past 20 years was examined for Anabaena resting spores (akinetes) in order to assess the utility of akinetes as a paleolimnological proxy. Sedimentary akinetes confirmed the past existence of Anabaena in water, but did not show a direct correlation with the amount of Anabaena spp. in water samples. The amount of planktonic Anabaena spp. correlated with total phosphorus and nitrogen concentrations in Lake Pyhäjärvi, but the number of akinetes was considered to have a relationship with low nutrient concentrations and dominant bloom-forming cyanobacteria. Akinetes are probably suitable for low-resolution and long time scale paleolimnological investigations, where they provide information of past cyanobacteria that cannot be directly attained otherwise.     

Detection of Pfiesteria spp. by PCR in surface sediments collected from Chesapeake Bay tributaries (Maryland)

In 1997 blooms of Pfiesteria piscicida occurred in association with fish kills and human health problems in tributaries of the Chesapeake Bay (Maryland) and the scientific and media response resulted in large economic losses in seafood sales and tourism. These events prompted the Maryland Department of Natural Resources (MDNR) to begin monitoring for Pfiesteria spp. in water column samples. Real-time PCR assays targeted to the 18S rRNA gene were developed by our laboratories and utilized in conjunction with traditional microscopy and fish kill bioassays for detection of these organisms in estuarine water samples. This monitoring strategy aided in determining temporal and spatial distribution of motile forms of Pfiesteria spp. (i.e. zoospores), but did not assess resting stages of the dinoflagellates’ life cycle. To address this area, a 3-year study was designed using real-time PCR assays for analysis of surface sediment samples collected from several Chesapeake Bay tributaries. These samples were tested with the real-time PCR assays previously developed by our laboratories. The data reported herein suggest a strong positive association between presence of Pfiesteria spp. in the sediment and water column, based on long-term water column monitoring data. P. piscicida is detected more commonly in Maryland's estuarine waters than Pfiesteria shumwayae and sediment ‘cyst beds’ may exist for these organisms.     

Atomic coordinates for the chlorophyll core of a bacteriochlorophyll a-protein from green photosynthetic bacteria

Preliminary atomic coordinates are presented for the seven bacteriochlorophylls constituting the core of one subunit of the trimeric water soluble bacteriochlorophyll $\text{a}$-protein from the green photosynthetic bacterium $\text{Prosthecochloris aestuarii}$, strain 2K, formerly identified as $\text{Chlorobium limicola}$, strain 2K. The coordinates were derived from a 2.8 Å resolution electron density map based on four isomorphous heavy-atom derivatives, and adjusted to have stereochemically acceptable bond lengths and angles.     

Diversity of Francisella Species in Environmental Samples from Martha’s Vineyard, Massachusetts

We determined whether Francisella spp. are present in water, sediment, and soil from an active tularemia natural focus on Martha’s Vineyard, Massachusetts, during a multiyear outbreak of pneumonic tularemia. Environmental samples were tested by polymerase chain reaction (PCR) targeting Francisella species 16S rRNA gene and succinate dehydrogenase A (sdhA) sequences; evidence of the agent of tularemia was sought by amplification of Francisella tularensis-specific sequences for the insertion element ISFTu2, 17-kDa protein gene tul4, and the 43-kDa outer membrane protein gene fopA. Evidence of F. tularensis subsp. tularensis, the causative agent of the human infections in this outbreak, was not detected from environmental samples despite its active transmission among ticks and animals in the sampling site. Francisella philomiragia was frequently detected from a brackish-water pond using Francisella species PCR targets, and subsequently F. philomiragia was isolated from an individual brackish-water sample. Distinct Francisella sp. sequences that are closely related to F. tularensis and Francisella novicida were detected from samples collected from the brackish-water pond. We conclude that diverse Francisella spp. are present in the environment where human cases of pneumonic tularemia occur.     

Diatom assemblages in sediments of Lake Juusa, Southern Estonia with an assessment of their habitat

Diatom analysis of surface sediments and two sediment cores from different sedimentation areas of a small closed lake was undertaken with the aim of acquiring knowledge on the dependence of the distribution of diatom assemblages on lake bathymetry. Lake Juusa was selected for the study because we have for this lake a large data set about the lithological composition of sediments and macrofossil and cladoceran records for the Holocene. A high carbonate content (20–60%) in the sediment sequence indicates high carbonacity and relatively stable pH values during the Holocene. On the basis of comprehensive analysis, abrupt water-level fluctuations and changes in the trophic status were established. Results of this study showed that the fluctuations of the water-level were the leading factor determining the habitats of diatom assemblages in the lake. In the surface sediment samples planktonic species such as Cyclotella spp., Stephanodiscus spp. and Aulacoseira spp. had a depth optimum at 3–4 m and the most abundant periphytic taxa were distributed mostly at depths shallower than 3.5 m. The same regularity was established in sediment cores where a good correlation between planktonic species and lake water depth was found in sediments accumulated at water depths >4 m. Lake Juusa appears to be a proper site for detailed environmental reconstructions over the Holocene, and the results will give us a good opportunity to analyse the history of water-level fluctuations in other small Estonian lakes. Electronic Supplementary Material The online version of this article (doi:) contains supplementary material, which is available to authorized users. Handling editor: K. Martens     

Sequence of the region downstream of theVitreoscilla hemoglobin gene:vgb is not part of a multigene operon

The 1668 base pairs (bp) downstream of theVitreoscilla hemoglobin gene were sequenced in the hope of finding related genes that might be part of an operon. Instead, a sequence was found that constituted an open reading frame (ORF) of 569 amino acids (apparently the carboxy-terminal part of a larger ORF), in the direction opposite to the hemoglobin gene. This sequence was found to have 64% similarity with the 1685 by at the 3 end of theEscherichia coli uvrA gene. The inferred amino acid sequence of the Vitreoscilla DNA has 69% similarity with the corresponding sequence of theE. coli uvrA protein, with similarities of 90, 100, and 85% in the helix-turn-helix, C-terminal ATP binding, and C-terminal zinc finger domains, respectively. The distance between the 3 ends of theVitreoscilla hemoglobin anduvrA genes is 63 bp.     

Gliding motility of Peloploca spp., and their distribution in the sediment and water column of a eutrophic lake

Observations indicating gliding motility in the gas-vacuolate, filamentous organism Peloploca were made using microcapillary tubes. Tubes containing semi-solid agar, incubated in sediment cores gave good enrichments of Peloploca spp. The organisms, which had the form of helical bundles of filaments, were seen to corkscrew through the agar at up to 2–3 m s^-1.The vertical distribution of Peloploca spp. in the sediment and water column of a eutrophic lake was examined periodically during summer stratification. The organisms were confined to anoxic conditions in the sediment prior to stratification. With increasing anoxia in the hypolimnion, the population shifted upwards in the sediment, and towards the end of stratification, in the most reducing conditions, appeared in the lower hypolimnion. Anaerobically incubated sediment cores also showed the movement of the Peloploca population from sediment into the overlying water.It is suggested that the gliding motility and helical morphology of Peloploca bundles enable them to migrate through sediment in response to oxygen and Eh gradients, in addition to their use of gas vacuoles to adjust their position in the water column. The taxonomic implications of gliding motility in Peloploca spp. are discussed.     

Chemical composition of the cell wall in some green algae species

Cell walls of two strains ofChlorella vulgaris (from fresh water, F, and saline water, S) and ofKirchneriella lunaris contained various proportion of saccharides and proteins (highest percentage in dry matter was found inK. lunaris). They differed also in presence of individual monosaccharides (5 inC. vulgaris F, 8 inC. vulgaris S and 6 inK. lunaris) and amino acids (11 in C.vulgaris F, 6 in C.vulgaris S and 7 inK. lunaris). Common substances were rhamnose, cystine, proline, glutamic acid and leucine. Communicated by Z. ŠESTáK     

The complex effects of the invasive polychaetes Marenzelleria spp. on benthic nutrient dynamics

The effects of the polychaetes Marenzelleria sp. (Polychaeta, Spionidae), nonindigenous, rapidly increasing species in the Baltic Sea, on benthic nutrient fluxes, denitrification and sediment pore water nutrient concentration were studied in laboratory experiments using a flow-through setup with muddy sediment from coastal regions of the Gulf of Finland. In addition, different forms of sediment phosphorus (P), separated by chemical fractionation, were studied in three sediment layers. At a population density corresponding to about half the highest measured in the northern Baltic Sea, Marenzelleria sp. increased the fluxes of P and ammonium to the water column. No effect could be recorded for denitrification. Since the previously dominant species of the area, Monoporeia affinis, can enhance denitrification and lower the amount of dissolved P in the pore water, the replacement of M. affinis with Marenzelleria spp. may lead to increased P flux to the water column and decreased denitrification, further increasing the ammonium flux to the water column. However, sediment reworking by Marenzelleria spp. also oxidizes the surface sediment in the long run, improving its ability to retain P and support nitrification. Therefore, the impact of Marenzelleria spp. on sediment nutrient release may not be as drastic as the initial reactions seen in our experiments suggest.